Since the season finale "The Incident" the concept was been that Jacob is the good guy-the white light and his rival, the nemesis is the bad guy-the black light. But is it correct to believe in this concept? Look at the conservation between Jacob and his "nemesis".
JACOB: I take it you're here 'cause of the ship. ENEMY: I am. How did they find the Island? JACOB: You'll have to ask 'em when they get here. ENEMY: I don't have to ask. You brought them here. Still trying to prove me wrong, aren't you? JACOB: You are wrong. ENEMY: Am I? They come. They fight. They destroy. They corrupt. It always ends the same. JACOB: It only ends once. Anything that happens before that is just progress.
By this discussion between them it is right to assume that Jacob has allowed outsiders to reach the island, and it always ends the same. So, why is Jacob allowing this to continue, why bring people to the island if they end up killing which other. Look at 1954, with the Others killing US soldiers, the conflict that existed between the Dharma Intiative and the Others that ended with The Purge.
The conflict between the survivors of Oceanic 815 and the Others, there was been a lot of blood spoiled on the island. Jacob allows this to continue because it is progress, one can look at Jacob as a mad scientist. The outsiders presence has had a negative effect on the island. The Dharma Intiative with their experiments which lead to the 'Incident'.
Maybe the Nemesis is the good guy with Jacob the bad guy. Maybe the nemesis got tired of all this killing and the abuse that was been inflected on the island, which is being allowed by Jacob, and wants to stop it. All the nemesis wants is to end this insane experiment, and the only way to do this is find his loophole.
With Jacob gone, no one will be able to reach the island and all this death will end, and there will be peace on the island. Or maybe the Nemesis is the nemesis, the bad guy that wants to kill everybody. Any thoughts?